Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme

doi:10.1016/j.xplc.2022.100413

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	Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme
	Sun, Meiyu ; Zhang, Yanan 3; Zhu, Li 3; Liu, Ningning 3; Bai, Hongtong ; Sun, Guofeng 2; Zhang, Jinzheng ; Shi, Lei
刊名	PLANT COMMUNICATIONS
	2022
卷号	3 期号:6
关键词	Thymus quinquecostatus chromosome-level genome phylogenetics glandular secretory trichome monoterpenoids
ISSN号	2590-3462
DOI	10.1016/j.xplc.2022.100413
文献子类	Article
英文摘要	Thyme hasmedicinal and aromatic value because of its potent antimicrobial and antioxidant properties. However, the absence of a fully sequenced thyme genome limits functional genomic studies of Chinese native thymes. Thymus quinquecostatus Celak., which contains large amounts of bioactive monoterpenes such as thymol and carvacrol, is an important wild medicinal and aromatic plant in China. Monoterpenoids are abundant in glandular secretory trichomes. Here, high-fidelity and chromatin conformation capture technologies were used to assemble and annotate the T. quinquecostatus genome at the chromosome level. The 13 chromosomes of T. quinquecostatus had a total length of 528.66 Mb, a contig N50 of 8.06 Mb, and a BUSCO score of 97.34%. We found that T. quinquecostatus had experienced two whole-genome duplications, with the most recent event occurring similar to 4.34 million years ago. Deep analyses of the genome, in conjunction with comparative genomic, phylogenetic, transcriptomic, and metabonomic studies, uncovered many regulatory factors and genes related to monoterpenoids and glandular secretory trichome development. Genes encoding terpene synthase (TPS), cytochrome P450 monooxygenases (CYPs), short-chain dehydrogenase/reductase (SDR), R2R3-MYB, and homeodomain-leucine zipper (HD-ZIP) IV were among those present in the T. quinquecostatus genome. Notably, Tq02G002290.1 (TqTPS1) was shown to encode the terpene synthase responsible for catalyzing production of the main monoterpene product gamma-terpinene from geranyl diphosphate (GPP). Our study provides significant insight into themechanisms of glandular secretory trichome formation and monoterpenoid biosynthesis in thyme. This work will facilitate the development of molecular breeding tools to enhance the production of bioactive secondary metabolites in Lamiaceae.
学科主题	Biochemistry & Molecular Biology ; Plant Sciences
出版地	AMSTERDAM
WOS关键词	DE-NOVO IDENTIFICATION ; EXPRESSION ANALYSIS ; TERPENE METABOLISM ; SUPPLEMENT TREMBL ; PLANT ; SEQUENCE ; ANNOTATION ; ALIGNMENT ; INITIATION ; DIVERSITY
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
语种	英语
出版者	ELSEVIER
WOS记录号	WOS:000910923700003
资助机构	Strategic Priority Research Program of the Chinese Academy of Sciences [XDA23080603]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/28953]
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, Beijing Bot Garden, Beijing 100093, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources & Beijing Bot Garden, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Sun, Meiyu,Zhang, Yanan,Zhu, Li,et al. Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme[J]. PLANT COMMUNICATIONS,2022,3(6).
APA	Sun, Meiyu.,Zhang, Yanan.,Zhu, Li.,Liu, Ningning.,Bai, Hongtong.,...&Shi, Lei.(2022).Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme.PLANT COMMUNICATIONS,3(6).
MLA	Sun, Meiyu,et al."Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme".PLANT COMMUNICATIONS 3.6(2022).